Puzzles of the mind
by mushushy
Summary: With Tony missing presumed dead the team must fend off attacks by Loki and his mystery associate. But is there more to what Loki is doing then meets the eye. Pepperony.
1. Chapter 1

**Puzzles of the mind.**

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**I do not own Iron Man or the rest of the Avengers gang.**

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**Chapter 1**

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Tony was having a perfect night alone with Pepper; it had been about half a year since the incident with the chuitari invasion. In those month the Stark tower was repaired and reopened as the Avenger tower. Of cause it came with the drawback of having to house the superheroes giving Tony a headache as the team settled in to their own floor. Since it was still technically Tony's building that meant that he could pick the penthouse floor. He had also tried to theme each room the liking of the individual. Although each had a separate room on different floors; they still had to share the kitchen and entertainment room between themselves. Tony of cause used the excuse of since he was the only one with a relationship the he had a separate floor for himself and Pepper. Whereas the rest of the avengers had to share the next few floors below him.

There had been a few incidents that had been really embarrassing for Pepper while Tony shrugged it off saying things like that happened, one of the most embarrassing one was when Bruce had walked in on them in Tony's lab while they were having mind blowing sex as Tony would say. Which prompted Bruce to walk straight out again with a blank face, the oblivious pair didn't even notice him enter or leave. The other avengers minus Tony of cause found him sitting there staring at the wall with no expression on his face it had taken a good half an hour for him to speak again but he never looked at Pepper again without blushing. Jarvis solved this problem by locking any door while they were like that or he would warn the others not to enter at that particular time and come back an hour or so later.

As Tony relaxed back into his sofa; Pepper leaned back resting her head on his chest just above the ark reactor. They had finished a nice dinner and were ready to watch a movie probably something involving with Will Smith as Pepper had a slight crush on him. They had managed to watch about twenty minutes or so before Tony's phone went off with the tune from an ACDC song. Noticing that Pepper was asleep on him he quickly saw that it was Shield calling him causing him to frown as he was supposed to have a night off. He switched it off. He would have to have a word with Fury about the definition of what a night off means.

Tony felt Pepper's phone on the couch vibrate as a call came in. Now he was starting get annoyed knowing that it was ether Fury or Hill ringing to get Pepper to send him off to the helicarrier for another mission or something. Just to try and prove a point he switched her phone off too and placed them on the side table without waking Pepper up. He was sure that they could survive without him for one night without the world coming to an end. Hopefully they would get the message and leave them alone for the night. Luck however was not on his side as Jarvis voice alerted him to Fury's constant attempts to contact him. Sighing Tony tried to slip out underneath Pepper without waking her he failed miserably as she opened her eyes and looked up at him with a pouting face. He knew that she was not going to like what he had to say so instead he hugged her tight not wanting to let her go again.

Finally releasing her from the hug he said to Jarvis. "Prepare the suit."

"At once sir" The AI replied.

"Tony do you have to go?" Pepper sighed holding onto his arm preventing him from leaving.

"Yeah Pep I do. But don't worry I will be back before you know it. I will give Fury a piece of my mind don't you worry." Tony said.

"Be sure that you do." She said letting go of his arm and watched him walk out of the room.

Going through the start procedure, Tony asked Jarvis to contact Fury knowing that he better check in before Fury has a fit. Fury answered with the usual annoyed voice.

"There had better be a really good reason that you have been ignoring my phone calls tonight Mr Stark."

"Yeah there is. I told you that tonight was my night off with Pepper. It's not my fault that you didn't listen." Tony said slightly annoyed at Fury for inferring that this was his entire fault.

"I had no other choice as the rest of the avengers were already there and are having difficulty containing the robots. Considering that it robotics were kind of your area of expertise we figured that you might be useful in helping defeat them." Fury explained.

Knowing that what Fury said made sense Tony couldn't fault the man for calling him away from his beloved Pepper. But just because it made sense didn't mean that he would go easy on the man as he really was having a great night in with Pepper before being called away. Oh he would make the one eyed pirate pay later. As the ironman suit assembled around Tony he was thinking the best way to go about this. Should he contact the team before anything else or should he just blast his way in to the fray.

Getting Fury on the earpiece he asked what kind of robots they were and who had sent them in the first place turns out that they had dealt with them before. The Doom bots sent by Dr Doom had attacked the USA a few months ago. Most people thought that the good Dr was defeated but what they didn't count on was his connections with some rich people which managed to get him released from prison. Instead of being rehabilitated he must have gone ahead and built these instead. Joy.

It turns out that the com units that the team were using were being jammed so Fury couldn't tell them that he was coming. Hopefully when he flew closer to the battle he would be able to contact them and see what the situation is like. Flying closer Tony could see the smoke cloud that indicated that there was the battle was he could see the Hulk smashing away down below. He didn't see anyone else as he flew closer to the centre of the battle taking out some doom bots as he went with his repulses.

Trying to get a fix on the other team members he tried the coms finding that they were still being jammed. Fuck! Now what? Should I waste time meeting up with Cap and the others or should I just go straight to the source of the problem. Yeah let's just take out the controller so I can go back to Pepper and try to forget about everything except for her.

"JARVIS do a scan of the area and check for any signal pertaining to the Doom bots, oh and see what you can do about the coms" Tony asked the AI. Where the fuck was everyone?

"Yes sir connecting to the oracle grid now." The AI replied.

As the AI searched the area for any sign of the signal origan Tony was busy fighting of the hoard of Doom bots that were in his immediate area. Still having no contact with the team was making him edgy. What if one of them were injured or needed help him had no way of knowing. Shaking his head he waited for JARVIS to get back to him with the information that he needed but until then he continued to destroy all the bots that came at him.

"Sir there is a positive match to the signal used by the Doom bots; it's in a building 1km to your right. There is an indication that there are people guarding the device but there is no way to know how many there might be sir." JARVIS piped up.

"Just in time J." Tony said.

As the information filtered across Tony's heads up display; he set a course heading towards the building holding the device he needed to destroy. Getting his first real look at the building he could see that it was several stories' high apartment building that was derelict and made of bricks. Engaging the heat senses on his HUD Tony saw that there were at least 20 or so people though out the building, two at the entrance of the building and the rest were situated on the second floor. How Dr Doom managed to get them to work for him Tony didn't know but he wouldn't go easy on them spotting a window that he could fit through Tony headed into the building at full speed smashing though the window showering the ground below.

Immediately upon entering the building he was shot at with machine guns, this whole situation was starting to annoy him, why did this have to happen when he was having a great night with Pepper. Getting a shot off at the direction of the computers set up to scramble the com signal and disable the Doom bots, Tony didn't get a chance to know if he hit anything important as he was inundated with both Doom bots and the people in the building guarding the device. Fighting them off had his power steadily declining as he shot of his unibeam to dislodge the doom bot clinging to the front. He would need to get another reactor when this was all over.

As he was fighting he didn't see the Doom bot sneaking up on him from behind, the first indicator that there was something wrong was the grinding metal sound and searing pain as the bot ripped parts of the back off his iron man suit and managing to get a claw in. Powering his thrusters he rammed straight backwards and into the wall dislodging the bot from his back. Groaning Tony quickly turned and fired a shot off spitting the bot that injured him in half. He knew that he needed to get his back seen too but first he needed to destroy all the electronics in the room, there just seemed to be an endless supply of the bots. The worst thing was that he didn't know if Dr Doom was around the building somewhere or was he out there fighting the rest of his team.

The rest of Doom's people fell easily to his shots, the Doom bots not so much. Not giving up he ploughed through the last ten remaining bots leaving him all alone in the room. Making his way over to the control panel he searched though the data to see if he could track where Dr Doom had set up his operation but with no luck. Taking a few steps backwards he held up both his hands and let of a couple of shots with his repulses straight at the control panel. What he wasn't counting on was that there was one doom bot still functioning, it made its way up behind Tony and just before the shots destroyed the control panel the Doom bot latched itself onto Tony's helmet and squeezed.

Shooting pain ran though out his head as his helmet was crushed inwards cutting into his head, giving a yell of pain Tony fell down to one knee and clutched his head in his hands. Unfortunately what he had no way of knowing, was that there was a built in self-destruct that was triggered by the destruction of the control panel, a little revenge from the Doctor if anyone destroyed it. The bombs were designed to bring the building down with the person trapped underneath it. Any normal person that wasn't wearing armour would probably be killed, so since Tony was wearing his Iron Man suit he didn't instantly become crushed to death.

The instant that Tony destroyed the control panel, there was a rumble as the building shook from the explosives that were triggered. A few seconds later the floor that he was standing on collapsed sending Tony yelling as he fell with the rest of the building coming down on him, not that Tony was too aware of what was going on as he was in a haze of pain. When Tony came to all he could see was black, he couldn't move a single finger let alone a leg or an arm. Panicking Tony started to try and struggle but it was impossible when everything ached and nothing moved. He could barely breathe as the crushing weight could be felt even with the suit on; _oh I am going to kill Fury when I got out of this._

"Jarvis are you there?" Tony groaned.

"…."

"Jarvis?" Tony asked again.

"…Syst…..Error….shut…own." Jarvis's said.

"Oh don't do that…come on Jarvis; Jarvis? Fuck!" Tony shouted.

_Fuck my helmet must be damaged too much; I need to get a message to the team and let them know that I'm under here. _Groaning he tried to keep his eyes open but the blood lose and the pain was too much, he lost the fight to stay conscious as everything went black his last thoughts was _Pepper is going to kill me._

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**AN: I hoped you liked the beginning, I will continue to post them as I write them. Please tell me what you think as I love reviews. To all those people waiting on the sequel to Time Warp, I'm still writing it so don't worry I haven't forgotten you. Till next time.**

**Mushushy.**


	2. Chapter 2

**Puzzles of the mind.**

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**I do not own Iron Man or the rest of the Avengers gang.**

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**Chapter 2**

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The Avengers minus Tony made their way back to Stark tower; each of them wanted to wash up; eat some dinner and head to bed for rest that was needed after fighting those damn doom bots. The avengers exited the Quinn jet sitting on the helipad and made their way into the building. They expected to see Tony and Pepper rest in the lounge room waiting to welcome them to come back. The TV was on but there was no sign of anyone in the room. Frowning the avengers walked further into the room, they knew that this was Tony's night off and that they really should leave the billionaire in peace with the woman that he loved but something was not sitting right with them.

All the times that Tony had stayed behind on missions he was always were there to meet them once they returned. So to see that there was no Tony waiting with his cheery attitudes and his smirks about not being trenched in slime and other things; it just felt wrong. Glancing at the coffee table in front of the lounge Clint saw both Tony's and Pepper's phones sitting there. He elbowed Natasha and raised his eyebrows suggestively. Natasha snorted her amusement which caused the others to look at her in confusion. _Oh how was she supposed to explain this to Thor let alone the Cap without breaking his innocence? _

"Considering both of the cell phones that are sitting here I think that Pepper and Tony are having some alone time." She said finally.

"Come let us gather our missing Avenger and celebrate our victory." Thor boomed happily oblivious to Clint sniggering and Natasha face palming.

"I think that Tony would prefer to celebrate in the morning as would I. I'm to worn out." Bruce said rescuing the assassin from her misery.

"Ok my friend but tomorrow we shall feast to VICTORY!" Thor said shouting the last word.

"Hey guy's; how was the battle?" A voice appeared behind them.

"Pepper! Sorry I don't think that Thor has a low volume. So you must have guessed that we won." Natasha said dryly looking at the thunder god with disapproval.

"No it's alright I just had to freshen up a bit." She said with a bush creeping up her face.

"So you wore out Tony already?" Clint asked smirking.

"What?" Pepper asked confused.

"Just ignore Clint, so where's Tony?" Bruce asked.

"I don't understand he was with you guys." Pepper replied shaking her head.

"No he wasn't; it was his night off." Natasha said frowning.

"Yes but Fury rang up saying that you guy's needed help, and so he flew off an hour ago." Pepper said her eyes widening in panic.

"I didn't see the man of Iron out there." Thor boomed shaking he's head.

"You don't think?" Clint turned to Natasha.

"No he would have contacted us." Natasha said shaking her head.

"Something was blocking our coms."

"And the Doombot's did seem to turn themselves off for no apparent reason."

"Oh my god!" Bruce exclaimed.

"So where is he then? He should have beaten us back here." Clint added.

Listening to this conversation Pepper started to panic more and more. There was a feeling that something was wrong; deeply wrong. If they hadn't seen Tony; did he even contact them before wading in? There was one way to find out.

"JARVIS!" Pepper called out.

"…My apology Miss Potts I seem to have lost contact to the Iron Man armour and I am unable to reconnect." The AI said sadly.

"What does that mean?" Steve asked confused.

"It means that Tony's in trouble." Pepper said quietly.

"We need to find the man of Iron!" Thor boomed from behind everyone.

"JARVIS are you able to track Tony?" Natasha asked.

"The tracking chip has been disabled. I have the last position that it broadcasted from."

The Avengers plus Pepper piled into the Quinn jet and power it up, it didn't take long till they were at the location that JARVIS had sent to the on board computer. Pepper was sitting there with her leg jiggling up and down in nervous energy, no matter what calm words Bruce was saying didn't seem to be getting through to her. In all honesty she was trying to block them out. Steve with his guilty looking stare could only be put up with for so long. All she wished was to land this jet to where Tony was standing healthy and whole. She doubted it was true, otherwise he would have at least checked in at some point. But she could dream right?

Pepper could help but think if she had told him to ignore both the phones when they rang; she figured he had picked it up so it didn't disturb her. If he didn't pick it up then they wouldn't be in this mess in the first place. It was all her fault. There was only one reason why JARVIS would lose contact with the suit and that was if the suit's helmet was damaged. The helmet that held Tony's head. Her heart started to beat faster as she felt the jet landing; ignoring Steve's protest, Pepper stood up heading to the ramp and waited for the doors to open. It didn't take long for them to open to the disastrous pile of rubble. She gasped at the sight of the deviation; her heart sank realizing that Tony was underneath the rubble. _Oh god Tony! Please hang on! _

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The flight to the last known location of Tony was to slow in Clint's opinion even though they were flying as fast as possible. They had alerted Fury and SHEILD to the potential situation. Fury had admitted sending Iron Man due to the com problems and that he hadn't heard anything from Tony since his original phone call. Fury told them to check it out as he organised a couple of teams to help them if there was anything wrong. Nearing the location, Clint couldn't help but frown. There was just a pile of rubble. Giving a shout buck to Natasha brought her to the front of the jet where she could see the state of what used to be a building. Concentrating on landing as close as possible Clint sent a quick prayer that Tony was still alive.

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The minute that they had boarded the Jet, Natasha set about trying to help keep Pepper calm but she could tell that she wasn't helping; neither was Bruce. Knowing Pepper she's probably blaming herself for letting Tony fly off into battle on their night off. There was not much that they could say that would help her even if she was listening to them in the first place. Clint gave her a shout from the front, so leaving Pepper in Bruce's hands Natasha made her way to the co-pilot seat and looked out the window. What greeted her were the remains of a brick building. If Tony was under all of that then it was a problem. How to get him out without damaging him further? They would defiantly need SHIELD rescue teams.

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Steve couldn't help but feel useless, He couldn't help fly the jet, he couldn't help comfort Pepper, he couldn't do anything to help Tony's situation. All he could do was wait. All he could hope for was that Tony was still alive and snarky as ever. If he had been a better leader and Known that Tony had joined the battle then maybe he could have prevented this. Or not; Tony was stubborn when it came to taking orders. They've had their disagreements of how to proceed into battle and normally had large arguments afterwards but if he had lost another friend in battle he didn't know what to do. So all he could do was wait and hope; a hope that was shattered when he caught sight of the rubble.

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Thor had been in many battles, even some that he had lost friends to, but not knowing whether or not the Man of Iron was alive or not was difficult to deal with. The first time he had met the man of Iron he didn't know anyone more arrogant and disrespectful but over time he had grown fond of the man. After all Tony had welcomed him into his home and showed him how to work machines around the home. Thor sighed knowing the Lady Pepper didn't need his assistance at that time he stayed out of the way silently wishing the Jet to travel faster. His first look at the rubble which contained Iron Man his heart couldn't help but sink.

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Even though Pepper didn't seem to be listening to a word he said; Bruce kept at it as it was helping stop him from hulking out. Enclosed spaces didn't help but the fact that his friend might be in trouble seemed to make it worse. Bruce was close to letting the Hulk out. If anything had happened to Tony while they were oblivious to their teammate's plight he didn't think that he would be able to prevent a Hulk out. The other guy was upset and raging to be let loose. The thought that he could harm someone in the jet kept him at bay. Bruce let out a sigh as the jet came to a stop and the doors to open. He let Pepper run out the door before following her with the rest of the Avengers right behind him. Seeing the amount of rubble he didn't think that anyone could survive this. He couldn't contain the Hulk anymore. With a ripping sound and a thunderous roar the Hulk was unleased.

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Pepper ran out of the Jet screaming Tony's name in the hope that he was still alive. There was no answer except for a huge roar from the hulk behind her. She didn't blame Bruce for losing control and letting the Hulk out but this wasn't a job for brute force. One wrong move and the Hulk could crush Tony. Plus they may need Bruce's medical knowledge as Tony seemed to be danger prone getting hurt the most out of all the avengers. This could end badly if they made the wrong move, but she knew better. Making her way calmly to the Hulk she stood in front of her as he looked down snorting angrily.

"HULK SMASH!" He bellowed into the air.

"Hulk you can't smash you might hurt Tony, please stay here." Pepper begged making the big green giant hesitate.

"HULK WAIT!" He said after a moment.

"Thank you Hulk." Pepper replied.

"You're welcome." He rumbled shocking everyone there.

"Ok every spread out and search for any sign of Tony or his suit but stay in sight. Clint get in contact with SHEILD tell them to send more search teams were going to need it." Steve ordered.

It wasn't long until they were stumbling through the rubble looking for any sign of Tony while the Hulk grumbled from the sideline. The SHEILD search teams turned up with one very angry Fury in tow. The team were surprised to see him as he hardly left his Helicarrier anymore. As Natasha explained the situation to Fury SHEILD had set up a perimeter around the few blocks so civilians couldn't get through; or more importantly the news crews. It would do no one any good if the world found out that Tony Stark was missing and possibly injured.

With those added teams it would make searching a lot quicker but not quickly enough for Pepper. She had been madly scrambling around searching for any sign of Tony but so far there was nothing. She was determined to not breakdown and cry it wouldn't do Tony any good and it certainly wouldn't do herself any good. Noticing something out of the corner of her eye she step closer noticing what looked like a clawed hand. She gave a shout to Steve who was the nearest person to her, as he made his way over to her; Pepper began to dig the claw out of the rubble. She managed to tug it free just in time for Steve to arrive. She thought that he muttered something along the line of Doombot but she wasn't really paying attention. Pepper was more concerned with the red and gold paint on the claws of the hand. She could never mistake what those two colours represent; Tony and his Iron Man.

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**AN: Hello to you all I want to thank everyone who reviewed, pressed favourite and started following this story. It really means the world to me when I see them in my inbox. Hope your liking the story so far if so; give me a shout. If you have any comments I welcome them to try to be a better writer. Please ignore the re-posting of chapter one as I had to fix a few problems with it. Till next time. :D**

**Mushushy.**


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